Genetic material, such as DNA and RNA from humans and other organisms, is often analyzed for nucleotide sequence, genetic-disease-causing mutations, or for single nucleotide polymorphisms (SNPs). Analysis often occurs after the DNA is isolated from cells and amplified using any of a number of amplification methods, such as the polymerase chain reaction (PCR), or the ligase chain reaction (LCR), among others. After DNA amplification, millions of identical copies of each DNA fragment are present in the sample fluid. These amplified fragments are then separated and concentrated into DNA bands containing fragments of identical length using either slab gel electrophoresis (SGE) or capillary gel electrophoresis (CGE).
A number of methods and instrument-based systems currently detect DNA sequences, genetic mutations, or SNPs after completion of DNA amplification and/or CGE or SGE. These include a number of DNA hybridization methods presently used in research protocols and in commercial assay systems. However, these systems have long assay times, require expensive reagents, and must be performed by highly trained technicians. In addition, some of these systems are not very sensitive and specific in detecting the presence of mutations or SNPs, particularly mutations involving stable mismatches. Finally, some of the methods are limited to low multiplex assays. In other words, the methods may only be used to analyze one, or at most a few nucleic acid fragments at a time.
An invention that quickly and efficiently determines the presence of mutations or SNPs, that minimizes cost, minimizes the use of technician time, and allows multiplex detection of many mutations at one time would be useful. In addition, it would also be useful to have a method that quickly identified nucleic acid sequences containing stable mismatches. Such a method would be of particular use in detecting nucleic acid mutations that result in genetic diseases.